"My expectation is that Australia will have a very strong and warm relationship with Indonesia, as we have had in the past," he said.

Labor had warned it could be difficult for Australia to normalise ties with its neighbour if the opportunity was not seized with Dr Yudhoyono, who will stand down in October after ten years at the helm.

But it's hoping a new leader will aid that process.

"We hope the election of new president will provide a circuit breaker for a better relationship with Indonesia," Opposition Leader Bill Shorten said.

Mr Joko said the first leaders to congratulate him were Dr Yudhoyono and Vice-President Boediono.

Then the prime ministers of Singapore and Australia called, he told reporters in Jakarta.

"President Obama called at 11am," Mr Joko said.

"We want to strengthen the relationship between Indonesia-America, Indonesia-Singapore and Indonesia-Australia."

Meanwhile, the loser of the presidential ballot, Prabowo Subianto, has vowed to challenge the result in the country's constitutional court.

His team on Wednesday reeled back his withdrawal from the race, saying he had done so only from the counting process and remains a candidate.